My Perfect setup (all emulators work perfectly):
Robert Broglia emulators - Paid (NES.emu, Snes9x EX+, MD.emu, NEO.emu, NGP.emu, GBA.emu, GBC.emu, PCE.emu)
-Used for NES, SNES, MegaDrive, NeoGeo, NeoGeo Pocket, GBA, GB/GBC.
ePSXe - Paid
-Used for playstation emulation
Mupen64Plus AE, Tendo 64 - Paid
-Used for N64 emualtion. I use Tendo 64 for games which do not work on mupen64 such as Blast Corps also Yoshi Story is laggy in mupen64 but plays perfectectly using Tendo64 using GLES-2.0 plugin (Tendo 64 is very good as its has many plugin and emulation profiles) between the two I have been able to play every single N64 game I have.
DraStic DS Emulator - Paid
-Used for Nintendo DS
aFBA, MAME4droid (0.139ui), MAME4droid (0.37b5
-Used for MAME/Arcade emulation. I mainly use aFBA as this plays all the MAME/ARCADE games I have even NEOGEO games, but its good to have the others just in case
-I just keep this as a backup in case I ever come across a situation where a game does not work on any of the above emulators.
With my setup I have been able to play every single game I have (100GB worth of games for all systems)